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- PDB-8pn4: transcription factor BARHL2 bound to DNA sequences -

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Basic information

Entry
Database: PDB / ID: 8pn4
Titletranscription factor BARHL2 bound to DNA sequences
Components
  • (DNA) x 2
  • BarH-like 2 homeobox protein
KeywordsTRANSCRIPTION / transcription factor / DNA-binding / protein-DNA complex / DNA-binding domain
Function / homology
Function and homology information


amacrine cell differentiation / cell fate determination / regulation of axon extension / positive regulation of translation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron migration / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II ...amacrine cell differentiation / cell fate determination / regulation of axon extension / positive regulation of translation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron migration / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / chromatin / nucleus
Similarity search - Function
: / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / DNA / DNA (> 10) / BarH-like 2 homeobox protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMorgunova, E. / Yin, Y. / Popov, A. / Taipale, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2025
Title: Interfacial water confers transcription factors with dinucleotide specificity.
Authors: Morgunova, E. / Nagy, G. / Yin, Y. / Zhu, F. / Nayak, S.P. / Xiao, T. / Sokolov, I. / Popov, A. / Laughton, C. / Grubmuller, H. / Taipale, J.
History
DepositionJun 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Apr 23, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BarH-like 2 homeobox protein
B: DNA
C: DNA
D: BarH-like 2 homeobox protein
E: DNA
F: DNA
G: BarH-like 2 homeobox protein
H: DNA
I: DNA
J: BarH-like 2 homeobox protein
K: DNA
L: DNA
M: BarH-like 2 homeobox protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,91014
Polymers66,85113
Non-polymers591
Water3,063170
1
A: BarH-like 2 homeobox protein
B: DNA
C: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8944
Polymers14,8353
Non-polymers591
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-13 kcal/mol
Surface area7370 Å2
MethodPISA
2
D: BarH-like 2 homeobox protein
E: DNA
F: DNA


Theoretical massNumber of molelcules
Total (without water)14,8353
Polymers14,8353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-12 kcal/mol
Surface area7530 Å2
MethodPISA
3
G: BarH-like 2 homeobox protein
H: DNA
I: DNA


Theoretical massNumber of molelcules
Total (without water)14,8353
Polymers14,8353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-15 kcal/mol
Surface area7400 Å2
MethodPISA
4
J: BarH-like 2 homeobox protein
K: DNA
L: DNA


Theoretical massNumber of molelcules
Total (without water)14,8353
Polymers14,8353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-14 kcal/mol
Surface area7220 Å2
MethodPISA
5
M: BarH-like 2 homeobox protein


Theoretical massNumber of molelcules
Total (without water)7,5091
Polymers7,5091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.426, 134.560, 64.491
Angle α, β, γ (deg.)90.00, 93.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BarH-like 2 homeobox protein


Mass: 7509.488 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BARHL2 / Plasmid: pET20A-SBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NY43
#2: DNA chain
DNA


Mass: 3638.379 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain
DNA


Mass: 3687.417 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: PEG 4000, sodium acetate,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.6→46.52 Å / Num. obs: 20553 / % possible obs: 99.5 % / Redundancy: 3.8 % / CC1/2: 0.985 / Rmerge(I) obs: 0.224 / Rpim(I) all: 0.135 / Rrim(I) all: 0.263 / Χ2: 0.96 / Net I/σ(I): 5.9 / Num. measured all: 78862
Reflection shellResolution: 2.6→2.72 Å / % possible obs: 97.5 % / Redundancy: 4 % / Rmerge(I) obs: 1.827 / Num. measured all: 9556 / Num. unique obs: 2416 / CC1/2: 0.285 / Rpim(I) all: 1.055 / Rrim(I) all: 2.114 / Χ2: 0.96 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→39.4 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.933 / SU B: 37.331 / SU ML: 0.377 / Cross valid method: THROUGHOUT / ESU R: 1.234 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27378 1034 5 %RANDOM
Rwork0.2434 ---
obs0.24507 19494 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.067 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å21.67 Å2
2---0.98 Å20 Å2
3---0.79 Å2
Refinement stepCycle: 1 / Resolution: 2.6→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2444 1942 0 170 4556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0114787
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173479
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.7356676
X-RAY DIFFRACTIONr_angle_other_deg0.4111.5858010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8525.618763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.053538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.76110488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.130.235820
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024264
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021060
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9072.0611130
X-RAY DIFFRACTIONr_mcbond_other0.9052.0611130
X-RAY DIFFRACTIONr_mcangle_it1.5543.6951403
X-RAY DIFFRACTIONr_mcangle_other1.5543.6951404
X-RAY DIFFRACTIONr_scbond_it1.0332.1343657
X-RAY DIFFRACTIONr_scbond_other1.0332.1343658
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6673.8255273
X-RAY DIFFRACTIONr_long_range_B_refined4.10638.2415955
X-RAY DIFFRACTIONr_long_range_B_other4.09738.215946
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 61 -
Rwork0.452 1377 -
obs--95.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.6728-0.8028-0.09436.5328-0.49295.1365-0.10080.0801-0.1968-0.03570.0916-0.14940.07350.09770.00920.09310.0082-0.11530.3334-0.00970.1687-6.4339-2.48636.3435
27.8629-2.02142.51814.0829-1.37173.6409-0.3718-0.54290.46260.4020.2614-0.1518-0.13380.13360.11040.09650.0456-0.120.3756-0.07760.2046-7.21695.930516.858
36.77520.58761.30039.50840.24563.84610.21870.1763-0.1419-0.4063-0.22060.1790.525-0.01320.00190.36660.1312-0.12180.3158-0.02750.0567-1.6074-26.800911.225
45.14061.0536-1.31345.19523.06167.09640.15480.02390.2296-0.25120.0352-0.87310.30281.0993-0.18990.42270.1251-0.04490.48150.12380.307810.4714-24.441417.3286
53.97631.3912-2.00037.30820.17186.19110.0643-0.1362-0.3234-0.17090.1097-0.5569-0.3669-0.1866-0.1740.12290.0207-0.1070.3450.0160.24813.59620.5714-0.7817
69.8711.4961-4.24082.94110.23373.5924-0.6280.3718-0.7359-0.30160.34-0.34170.16440.16010.2880.1467-0.0582-0.11950.454-0.00120.447312.961211.4033-10.6851
73.7201-0.3529-0.87646.7406-0.90627.81110.08430.28440.6016-0.53820.04160.4833-0.1548-0.6483-0.12590.2657-0.0172-0.21130.4306-0.01490.3126-12.079-16.7992-19.4162
81.7914-0.4974-3.05623.2036-0.0838.5745-0.29730.03560.0019-0.26970.2509-0.04620.6136-0.02160.04640.3212-0.0204-0.15590.4005-0.05390.1723-8.6068-29.5705-16.9509
96.68531.3586-3.20158.95041.88723.7814-0.40320.30780.0297-0.63050.111-1.02840.09050.56860.29220.4967-0.0709-0.04850.74670.00780.62966.9718-4.8022-22.4249
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A232 - 291
2X-RAY DIFFRACTION2B1 - 24
3X-RAY DIFFRACTION3D232 - 290
4X-RAY DIFFRACTION4E1 - 24
5X-RAY DIFFRACTION5G233 - 292
6X-RAY DIFFRACTION6H1 - 24
7X-RAY DIFFRACTION7J232 - 289
8X-RAY DIFFRACTION8K1 - 24
9X-RAY DIFFRACTION9M244 - 289

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